Yearly Archives: 2018

After two years of alpha- and beta-testing, we are glad to announce the official release of FishResp!

We tried to make FishResp suitable for every researcher interested in the analysis of raw respirometry data. Are you a fan of console or a graphical user interface? Do you work with fancy commercial respirometry systems or with your own DIY setup? Do you rely on this or that experimental design/methodological approach?

To suit all your needs, we developed both an R package and a cross-platform GUI application which are integrated with the majority of respirometry systems and have wide range of options for analyses of respirometry data. The preprint describing the software will be available in November 2018.

Integration with the majority of respirometry systems

Now, the software is able to import raw data from various intermittent-flow respirometry systems available in the market. Particularly, the output can be loaded to FishResp from following oxygen logger software: ‘AutoResp‘ (LoligoSystems); ‘Qbox-Aqua‘ (QubitSystems); ‘OxyView‘ (PreSens) and ‘Pyro Oxygen Logger‘ (PyroScience) used in couple with ‘AquaResp‘ (free software). Raw data obtained from DIY respirometry setups should be converted manually to the ‘FishResp’ format first and then can be loaded to FishResp as well.

This update could not be done without data contribution of Daniel Montgomery, Laura Almodovar-Acevedo and Stephen White. Thank for making FishResp better!

Diagnostic plots for linear regression analysis

The other important feature of the officially released version is implementation of diagnostic plots for linear regression analysis. Three types of diagnostic plots are available for both current and alternative lengths of selected slopes: “Residuals vs Fitted”, “Normal Q-Q”, “Scale-Location”. In addition, a user is able to remove poor-quality measurement phase(s) manually in the GUI application for specific trait and respirometry chamber.

List of other updates:

• ‘Qbox-Aqua’ is a new logger software implemented in the functions import.test and import.meas

• Optional increase of the wait phase (’W’) is available in the functions import.test and import.meas if the wait phase is absent or not long enough to eliminate non-linear change in DO concentration over time from the measurement phase (’M’) after shutting off water supply from the ambient water source.

• Implementation of diagnostic plots for linear regression analysis was added to the function QC.slope: “Residuals vs Fitted”, “Normal Q-Q”, “Scale-Location” for both current and alternative lengths of selected slopes.

• The new function rm.data removes manually measurement phases (’M’) which did not pass QC tests. For the GUI application, a new pop-up window has been developed for removing measurement phases (the button ‘Remove Data’).

A serious bug has been found in the source code which should be taken into account by all users worked with previous versions of FishResp (i.e. 0.1; 0.2; 0.3; 0.4). Specifically, the function calculate.MR converted incorrectly time units from seconds to hours which led to 3.6-fold underestimation of absolute and mass-specific metabolic rate. To fix wrong calculation of metabolic rate estimates, please multiply them by 3.6 times in the final dataset (excluding factorial metabolic scope and background respiration).

We thank Nicholas Carey, the developer of the R-package ‘respR‘, for comparing outputs of our packages and detecting this bug. Now, both ‘respR’ and FishResp show identical results with the same input data. We are also grateful to people who have found missing information in package documentation or minor bugs in the code over the last two years. All of them are fixed: source code, documentation and demo-data have been updated in the version 1.0.1.

Beta testing is over. The official release of the ‘FishResp’ software will be announced in October 2018.

As 8% of male population and around 0.4% of female population have some type of colour blindness, we decided to test both GUI application and graphs produced by the R package via colour the blindness simulators “Sim Daltonism” and “Color Oracle”. As a result, some colour changes have been implemented to the code in the R package, while the graphical interface has not been changed due to distinctive hues of different functional buttons (see the screenshot). We thank the anonymous reviewer of our manuscript devoted to the FishResp software for sharing this idea.

Major updates

• ability to import datasets with columns containing only NA or NaN values
• ability to import raw data with both decimal separators: “.” and “,”

Minor updates

• line “now” has been changed from green to red, while line “alter” has been changed from red to black in the function QC.slope
• words “now” and “alter” have been replaced by actual length of slopes (in sec) in the legend of the figure produced by the function QC.slope
• parameter “Weight” has been changed to “Mass” in the function input.info
• parameter “q” has been changed to “p” in the function extract.slope
• default value for the parameter “r2” in the function extract.slope has been changed from 0.9 to 0.95
• the bug with warnings occurred in the function extract.slope has been fixed

Both the R package and its GUI implementation were upgraded to the version 0.2.0. New options for import, correction and calculation of respirometry data suppose to make ‘FishResp’ a more flexible tool than before. In addition, several bugs and technical problems were revealed and fixed, which should improve the stability of the software. Please, see the list of updates below to get detailed information on the changes applied to the new version of ‘FishResp’.

Major updates

• seven new methods of slope extraction are integrated into the function extract.slope(including ones described in Chabot et al, 2016*)

• ‘progressive’ method for correction of background respiration was split into ‘linear’ and ‘exponential’ in the functioncorrect.meas

• ability to work with different date formats (DMY, MDY and YMD) and time formats (24h, AM/PM)

• two new functions convert.respirometry and convert.rMR were created to convert other DO units to acceptable ones. These functions represents modifications of the functions conv_o2 and DO.unit.convert from the packages ‘respirometry’ and ‘rMR’ packages, respectively.

GUI updates

• new extensions module for integration with other R packages, scripts and functions

• graphical interfaces for extensions ‘respirometry’ and ‘rMR’ (only converter functions have been used from those packages)

• opportunity to create a log file to record commands and error messages on the hard drive

Archives

Contact info

'FishResp' is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License, Version 3.

'FishResp' is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose. See the GNU General Public License for more details.